openminds.specimen_prep

In-depth metadata for the preparation of specimens (e.g. cell culture, surgical procedures, tissue slicing).

class CranialWindowPreparation(lookup_label=None, construction_type=None, custom_property_sets=None, description=None, dimension=None, end_time=None, inputs=None, is_part_of=None, outputs=None, performed_by=None, preparation_design=None, protocols=None, reinforcement_type=None, start_time=None, study_targets=None, id=None, data=None, space=None, release_status=None)

Bases: KGObject, CranialWindowPreparation

<description not available>

Parameters:

• construction_type (CranialWindowConstructionType) – no description available

• custom_property_sets (CustomPropertySet) – no description available

• description (str) – Longer statement or account giving the characteristics of the cranial window preparation.

• dimension (Circle, Ellipse, Rectangle) – no description available

• end_time (datetime, time) – no description available

• inputs (SubjectState) – Something or someone that is put into or participates in a process or machine.

• is_part_of (DatasetVersion) – Reference to the ensemble of multiple things or beings.

• lookup_label (str) – no description available

• outputs (SubjectState) – Something or someone that comes out of, is delivered or produced by a process or machine.

• performed_by (SoftwareAgent, Person) – no description available

• preparation_design (PreparationType) – no description available

• protocols (Protocol) – Plan that describes the process of a scientific or medical experiment, treatment, or procedure.

• reinforcement_type (CranialWindowReinforcementType) – no description available

• start_time (datetime, time) – no description available

• study_targets (AuditoryStimulusType, BiologicalOrder, BiologicalSex, BreedingType, CellCultureType, CellType, Disease, DiseaseModel, ElectricalStimulusType, GeneticStrainType, GustatoryStimulusType, Handedness, MolecularEntity, OlfactoryStimulusType, OpticalStimulusType, Organ, OrganismSubstance, OrganismSystem, Species, SubcellularEntity, TactileStimulusType, TermSuggestion, TissueSampleType, UBERONParcellation, VisualStimulusType, CustomAnatomicalEntity, ParcellationEntity, ParcellationEntityVersion) – Structure or function that was targeted within a study.

class TissueCulturePreparation(lookup_label=None, culture_medium=None, culture_type=None, custom_property_sets=None, description=None, end_time=None, inputs=None, is_part_of=None, outputs=None, performed_by=None, preparation_design=None, protocols=None, start_time=None, study_targets=None, id=None, data=None, space=None, release_status=None)

Bases: KGObject, TissueCulturePreparation

<description not available>

Parameters:

• culture_medium (ChemicalMixture) – no description available

• culture_type (CellCultureType) – no description available

• custom_property_sets (CustomPropertySet) – no description available

• description (str) – Longer statement or account giving the characteristics of the tissue culture preparation.

• end_time (datetime, time) – no description available

• inputs (TissueSampleState, TissueSampleCollectionState, SubjectGroupState, SubjectState) – Something or someone that is put into or participates in a process or machine.

• is_part_of (DatasetVersion) – Reference to the ensemble of multiple things or beings.

• lookup_label (str) – no description available

• outputs (TissueSampleState) – Something or someone that comes out of, is delivered or produced by a process or machine.

• performed_by (SoftwareAgent, Person) – no description available

• preparation_design (PreparationType) – no description available

• protocols (Protocol) – Plan that describes the process of a scientific or medical experiment, treatment, or procedure.

• start_time (datetime, time) – no description available

• study_targets (AuditoryStimulusType, BiologicalOrder, BiologicalSex, BreedingType, CellCultureType, CellType, Disease, DiseaseModel, ElectricalStimulusType, GeneticStrainType, GustatoryStimulusType, Handedness, MolecularEntity, OlfactoryStimulusType, OpticalStimulusType, Organ, OrganismSubstance, OrganismSystem, Species, SubcellularEntity, TactileStimulusType, TermSuggestion, TissueSampleType, UBERONParcellation, VisualStimulusType, CustomAnatomicalEntity, ParcellationEntity, ParcellationEntityVersion) – Structure or function that was targeted within a study.

class TissueSampleSlicing(lookup_label=None, custom_property_sets=None, description=None, device=None, end_time=None, inputs=None, is_part_of=None, outputs=None, performed_by=None, preparation_design=None, protocols=None, start_time=None, study_targets=None, temperature=None, tissue_bath_solution=None, id=None, data=None, space=None, release_status=None)

Bases: KGObject, TissueSampleSlicing

<description not available>

Parameters:

• custom_property_sets (CustomPropertySet) – no description available

• description (str) – Longer statement or account giving the characteristics of the tissue sample slicing.

• device (SlicingDeviceUsage) – Piece of equipment or mechanism (hardware) designed to serve a special purpose or perform a special function.

• end_time (datetime, time) – no description available

• inputs (SubjectState, TissueSampleCollectionState, TissueSampleState) – Something or someone that is put into or participates in a process or machine.

• is_part_of (DatasetVersion) – Reference to the ensemble of multiple things or beings.

• lookup_label (str) – no description available

• outputs (TissueSampleCollectionState, TissueSampleState) – Something or someone that comes out of, is delivered or produced by a process or machine.

• performed_by (SoftwareAgent, Person) – no description available

• preparation_design (PreparationType) – no description available

• protocols (Protocol) – Plan that describes the process of a scientific or medical experiment, treatment, or procedure.

• start_time (datetime, time) – no description available

• study_targets (AuditoryStimulusType, BiologicalOrder, BiologicalSex, BreedingType, CellCultureType, CellType, Disease, DiseaseModel, ElectricalStimulusType, GeneticStrainType, GustatoryStimulusType, Handedness, MolecularEntity, OlfactoryStimulusType, OpticalStimulusType, Organ, OrganismSubstance, OrganismSystem, Species, SubcellularEntity, TactileStimulusType, TermSuggestion, TissueSampleType, UBERONParcellation, VisualStimulusType, CustomAnatomicalEntity, ParcellationEntity, ParcellationEntityVersion) – Structure or function that was targeted within a study.

• temperature (QuantitativeValue, QuantitativeValueRange) – no description available

• tissue_bath_solution (ChemicalMixture) – no description available

class SlicingDevice(name=None, lookup_label=None, description=None, device_type=None, digital_identifier=None, is_part_of=None, manufacturers=None, owners=None, serial_number=None, usage=None, id=None, data=None, space=None, release_status=None)

Bases: KGObject, SlicingDevice

<description not available>

Parameters:

• description (str) – Longer statement or account giving the characteristics of the slicing device.

• device_type (DeviceType) – no description available

• digital_identifier (DOI, RRID) – Digital handle to identify objects or legal persons.

• lookup_label (str) – no description available

• manufacturers (Consortium, Organization, Person) – no description available

• name (str) – Word or phrase that constitutes the distinctive designation of the slicing device.

• owners (Consortium, Organization, Person) – no description available

• serial_number (str) – no description available

• is_part_of (Setup) – reverse of ‘has_parts’

• usage (SlicingDeviceUsage) – reverse of ‘device’

class SlicingDeviceUsage(lookup_label=None, device=None, generation_device=None, metadata_locations=None, oscillation_amplitude=None, placed_by=None, slice_thickness=None, slicing_angles=None, slicing_plane=None, slicing_speed=None, used_for=None, used_in=None, used_specimen=None, used_to_measure=None, used_to_record=None, vibration_frequency=None, id=None, data=None, space=None, release_status=None)

Bases: KGObject, SlicingDeviceUsage

<description not available>

Parameters:

• device (SlicingDevice) – Piece of equipment or mechanism (hardware) designed to serve a special purpose or perform a special function.

• lookup_label (str) – no description available

• metadata_locations (File, FileBundle) – no description available

• oscillation_amplitude (QuantitativeValue) – no description available

• slice_thickness (QuantitativeValue, QuantitativeValueRange) – no description available

• slicing_angles (QuantitativeValue, NumericalProperty) – no description available

• slicing_plane (AnatomicalPlane) – no description available

• slicing_speed (QuantitativeValue) – no description available

• used_specimen (SubjectState, TissueSampleState) – no description available

• vibration_frequency (QuantitativeValue) – no description available

• generation_device (EphysStimulus) – reverse of ‘generated_by’

• placed_by (ElectrodePlacement) – reverse of ‘devices’

• used_for (TissueSampleSlicing) – reverse of ‘device’

• used_in (CellPatching) – reverse of ‘devices’

• used_to_measure (Measurement) – reverse of ‘measured_with’

• used_to_record (Recording) – reverse of ‘recorded_with’